From cc1141aee1478a4450dbd3120c6f5575dbea325a Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Tue, 16 Dec 2025 15:43:57 -0500
Subject: [PATCH 01/41] feat: updated fastANI module to include proper
 reference and query file staging, added task.cpus to thread arg, created
 process stub, added optional tool outputs, and formatted input channels

---
 modules/nf-core/fastani/main.nf | 72 ++++++++++++++++++++-------------
 1 file changed, 43 insertions(+), 29 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index f6284538f9da..e9710b18bee0 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -9,11 +9,15 @@ process FASTANI {
 
     input:
     tuple val(meta), path(query)
-    path reference
+    tuple val(meta2), path(reference)
+    path ql
+    path rl
 
     output:
-    tuple val(meta), path("*.ani.txt"), emit: ani
-    path "versions.yml"               , emit: versions
+    tuple val(meta), path("*.txt")  , emit: ani
+    tuple val(meta), path("*.visual")   , optional:true, emit: visual
+    tuple val(meta), path("*.matrix")   , optional:true, emit: matrix
+    path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
@@ -21,30 +25,40 @@ process FASTANI {
     script:
     def args = task.ext.args ?: ''
     def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix2 = task.ext.prefix2 ?: "${meta2.id}"
+    def input_query = query ? "-q ${query}": "--ql ${ql}"
+    def input_reference = reference ? "-r ${reference}": "--rl ${rl}"
+    def out = query ?: ( reference ? "-o ${prefix}_v_${prefix2}": "-o ${prefix}_v_all"): ( reference ? "-o all_v_${prefix2}": "-o all_v_all" )
 
-    if (meta.batch_input) {
-        """
-        fastANI \\
-            -ql $query \\
-            -rl $reference \\
-            -o ${prefix}.ani.txt
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
-        END_VERSIONS
-        """
-    } else {
-        """
-        fastANI \\
-            -q $query \\
-            -r $reference \\
-            -o ${prefix}.ani.txt
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
-        END_VERSIONS
-        """
-    }
-}
+    """
+    fastANI \\
+        $input_query \\
+        $input_reference \\
+        --threads $task.cpus \\
+        $out
+    
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
+    END_VERSIONS
+    """
+
+    stub:
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix ?: "${meta.id}"
+    def prefix2 = task.ext.prefix2 ?: "${meta2.id}"
+    def input_query = query ? "-q ${query}": "--ql ${ql}"
+    def input_reference = reference ? "-r ${reference}": "--rl ${rl}"
+    def out = query ?: ( reference ? "-o ${prefix}_v_${prefix2}": "-o ${prefix}_v_all"): ( reference ? "-o all_v_${prefix2}": "-o all_v_all" )
+
+    """
+    touch ${out}.visual
+    touch ${out}.txt
+    touch ${out}.matrix
+
+    cat <<-END_VERSIONS > versions.yml
+    "${task.process}":
+        fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
+    END_VERSIONS
+    """
+}
\ No newline at end of file

From 8d54dba43dae0a634e34504f951d5806a33bd6ea Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 13:47:03 -0500
Subject: [PATCH 02/41] refactor: modified input/output options for fastANI and
 added stub test

---
 modules/nf-core/fastani/main.nf               |  39 ++---
 modules/nf-core/fastani/tests/main.nf.test    |  40 ++++-
 .../nf-core/fastani/tests/main.nf.test.snap   | 149 ++++++++++++++++++
 modules/nf-core/fastani/tests/nextflow.config |   5 +
 4 files changed, 208 insertions(+), 25 deletions(-)
 create mode 100644 modules/nf-core/fastani/tests/nextflow.config

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index e9710b18bee0..18e8ca3ec1c1 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -8,34 +8,33 @@ process FASTANI {
         'biocontainers/fastani:1.32--he1c1bb9_0' }"
 
     input:
-    tuple val(meta), path(query)
+    tuple val(meta),  path(query)
     tuple val(meta2), path(reference)
-    path ql
-    path rl
+    path(ql)
+    path(rl)
 
     output:
-    tuple val(meta), path("*.txt")  , emit: ani
-    tuple val(meta), path("*.visual")   , optional:true, emit: visual
-    tuple val(meta), path("*.matrix")   , optional:true, emit: matrix
+    tuple val(meta), path("*.txt")      , emit: ani
+    tuple val(meta), path("*.visual")   , optional:true , emit: visual
+    tuple val(meta), path("*.matrix")   , optional:true , emit: matrix
     path "versions.yml"                 , emit: versions
 
     when:
     task.ext.when == null || task.ext.when
 
     script:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def prefix2 = task.ext.prefix2 ?: "${meta2.id}"
-    def input_query = query ? "-q ${query}": "--ql ${ql}"
+    def args            = task.ext.args ?: ''
+    def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
+    def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all')
+    def input_query     = query ? "-q ${query}": "--ql ${ql}"
     def input_reference = reference ? "-r ${reference}": "--rl ${rl}"
-    def out = query ?: ( reference ? "-o ${prefix}_v_${prefix2}": "-o ${prefix}_v_all"): ( reference ? "-o all_v_${prefix2}": "-o all_v_all" )
-
+    
     """
     fastANI \\
         $input_query \\
         $input_reference \\
         --threads $task.cpus \\
-        $out
+        -o ${prefix}_v_${prefix2}.txt
     
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
@@ -44,17 +43,13 @@ process FASTANI {
     """
 
     stub:
-    def args = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def prefix2 = task.ext.prefix2 ?: "${meta2.id}"
-    def input_query = query ? "-q ${query}": "--ql ${ql}"
-    def input_reference = reference ? "-r ${reference}": "--rl ${rl}"
-    def out = query ?: ( reference ? "-o ${prefix}_v_${prefix2}": "-o ${prefix}_v_all"): ( reference ? "-o all_v_${prefix2}": "-o all_v_all" )
+    def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
+    def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all')
 
     """
-    touch ${out}.visual
-    touch ${out}.txt
-    touch ${out}.matrix
+    touch ${prefix}_v_${prefix2}.visual
+    touch ${prefix}_v_${prefix2}.txt
+    touch ${prefix}_v_${prefix2}.matrix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index a4318db49ee3..b2f67e55513a 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -7,7 +7,7 @@ nextflow_process {
     script "../main.nf"
     process "FASTANI"
 
-    test("FastANI") {
+    test("fastani - 1v1") {
 
         when {
             process {
@@ -16,7 +16,41 @@ nextflow_process {
                     [ id:'test' ],
                     file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
                 ]
-                input[1] = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
+                input[1] = [
+                    [ id:'test2' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
+                ]
+                input[2] = []
+                input[3] = []
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert process.success },
+                { assert snapshot(process.out).match() }
+            )
+        }
+    }
+
+    test("stub") {
+
+        options '-stub'
+
+        when {
+            process {
+                """
+                input[0] = [
+                    [ id:'test' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                ]
+                input[1] = [
+                    [ id:'test2' ],
+                    file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
+                ]
+                input[2] = []
+                input[3] = []
                 """
             }
         }
@@ -30,4 +64,4 @@ nextflow_process {
 
     }
 
-}
+}
\ No newline at end of file
diff --git a/modules/nf-core/fastani/tests/main.nf.test.snap b/modules/nf-core/fastani/tests/main.nf.test.snap
index dbb02572949e..62ebcf259dd8 100644
--- a/modules/nf-core/fastani/tests/main.nf.test.snap
+++ b/modules/nf-core/fastani/tests/main.nf.test.snap
@@ -1,4 +1,49 @@
 {
+    "fastani - 1v1": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                ],
+                "ani": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
+                    ]
+                ],
+                "matrix": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                ],
+                "visual": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.1"
+        },
+        "timestamp": "2025-12-17T13:46:06.970355559"
+    },
     "FastANI": {
         "content": [
             {
@@ -26,6 +71,110 @@
                 ]
             }
         ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.1"
+        },
         "timestamp": "2023-10-18T12:02:08.983912093"
+    },
+    "fastani - updates - fasta - fasta": {
+        "content": [
+            {
+                "0": [
+                    
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    
+                ],
+                "ani": [
+                    
+                ],
+                "matrix": [
+                    
+                ],
+                "versions": [
+                    
+                ],
+                "visual": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.1"
+        },
+        "timestamp": "2025-12-17T13:04:20.452047779"
+    },
+    "stub": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "1": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.visual:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "2": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.matrix:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "3": [
+                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                ],
+                "ani": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "matrix": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.matrix:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ],
+                "versions": [
+                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                ],
+                "visual": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test_v_test2.visual:md5,d41d8cd98f00b204e9800998ecf8427e"
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.1"
+        },
+        "timestamp": "2025-12-17T13:46:15.662109587"
     }
 }
\ No newline at end of file
diff --git a/modules/nf-core/fastani/tests/nextflow.config b/modules/nf-core/fastani/tests/nextflow.config
new file mode 100644
index 000000000000..ad8804bdb64a
--- /dev/null
+++ b/modules/nf-core/fastani/tests/nextflow.config
@@ -0,0 +1,5 @@
+process {
+    withName: FASTANI {
+        ext.args = "--matrix"
+    }
+}

From fd58eb351b4208507ba45ccad55212ebd64de0c3 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 13:52:41 -0500
Subject: [PATCH 03/41] chore: updated meta.yml

---
 modules/nf-core/fastani/meta.yml | 62 ++++++++++++++++++++------------
 1 file changed, 40 insertions(+), 22 deletions(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index 1b52160b136a..fb9b70deb26c 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -1,55 +1,73 @@
 name: fastani
-description: Alignment-free computation of average nucleotide Identity (ANI)
+description: Alignment-free computation of Average Nucleotide Identity (ANI)
 keywords:
   - genome
   - fasta
   - ANI
+
 tools:
   - fastani:
-      description: FastANI is developed for fast alignment-free computation of whole-genome
-        Average Nucleotide Identity (ANI).
+      description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
       homepage: https://github.com/ParBLiSS/FastANI
       documentation: https://github.com/ParBLiSS/FastANI
       tool_dev_url: https://github.com/ParBLiSS/FastANI
       doi: 10.1038/s41467-018-07641-9
       licence: ["Apache-2.0"]
       identifier: biotools:fastani
+
 input:
   - - meta:
         type: map
-        description: |
-          Groovy Map containing sample information
-          e.g. [ id:'test', single_end:false ]
+        description: Groovy Map containing sample information for the query
     - query:
         type: file
-        description: Fasta file(s) to be queried
+        description: Fasta file to be used as the query
         pattern: "*.fasta"
-        ontologies: []
-  - reference:
+  - - meta2:
+        type: map
+        description: Groovy Map containing sample information for the reference
+    - reference:
+        type: file
+        description: Fasta file to be used as the reference
+        pattern: "*.fasta"
+  - ql:
+      type: file
+      description: File containing a list of query fasta paths
+      pattern: "*.txt"
+  - rl:
       type: file
-      description: Fasta file(s) to be used as reference for the query
-      pattern: "*.fasta"
-      ontologies: []
+      description: File containing a list of reference fasta paths
+      pattern: "*.txt"
+
 output:
   ani:
     - - meta:
           type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test', single_end:false ]
-      - "*.ani.txt":
+      - "*.txt":
           type: file
-          description: Results of the query
-          pattern: "*.ani.txt"
-          ontologies: []
+          description: ANI results file
+          pattern: "*.txt"
+  visual:
+    - "*.visual":
+        type: file
+        optional: true
+        description: FastANI visualization output
+  matrix:
+    - "*.matrix":
+        type: file
+        optional: true
+        description: ANI matrix output
   versions:
     - versions.yml:
         type: file
-        description: File containing software versions
+        description: File containing software version information
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+          - edam: http://edamontology.org/format_3750
+
 authors:
+  - "@Ethan-Hetrick"
   - "@abhi18av"
 maintainers:
-  - "@abhi18av"
+  - "@Ethan-Hetrick"
+  - "@abhi18av"
\ No newline at end of file

From ae6a3c14514f329e5e9b3085ae1c7c42ea5fbee2 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 14:20:31 -0500
Subject: [PATCH 04/41] fix: corrected meta.yml

---
 modules/nf-core/fastani/meta.yml | 35 +++++++++++++++++++++++---------
 1 file changed, 25 insertions(+), 10 deletions(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index fb9b70deb26c..5ab3cc5a4475 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -17,8 +17,10 @@ tools:
 
 input:
   - - meta:
-        type: map
-        description: Groovy Map containing sample information for the query
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
     - query:
         type: file
         description: Fasta file to be used as the query
@@ -43,20 +45,33 @@ output:
   ani:
     - - meta:
           type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
       - "*.txt":
           type: file
           description: ANI results file
           pattern: "*.txt"
   visual:
-    - "*.visual":
-        type: file
-        optional: true
-        description: FastANI visualization output
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.visual":
+          type: file
+          optional: true
+          description: FastANI visualization output
   matrix:
-    - "*.matrix":
-        type: file
-        optional: true
-        description: ANI matrix output
+    - - meta:
+          type: map
+          description: |
+            Groovy Map containing sample information
+            e.g. [ id:'test' ]
+      - "*.matrix":
+          type: file
+          optional: true
+          description: ANI matrix output
   versions:
     - versions.yml:
         type: file

From 07024b8cb24d3c0f6197fe0eb26202484c04f113 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 14:50:15 -0500
Subject: [PATCH 05/41] fix: corrected file formats

---
 modules/nf-core/fastani/main.nf  | 2 +-
 modules/nf-core/fastani/meta.yml | 4 ----
 2 files changed, 1 insertion(+), 5 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 18e8ca3ec1c1..f33cbbc1d5bb 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -56,4 +56,4 @@ process FASTANI {
         fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
     END_VERSIONS
     """
-}
\ No newline at end of file
+}
diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index 5ab3cc5a4475..b706814f994f 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -4,7 +4,6 @@ keywords:
   - genome
   - fasta
   - ANI
-
 tools:
   - fastani:
       description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
@@ -14,7 +13,6 @@ tools:
       doi: 10.1038/s41467-018-07641-9
       licence: ["Apache-2.0"]
       identifier: biotools:fastani
-
 input:
   - - meta:
           type: map
@@ -40,7 +38,6 @@ input:
       type: file
       description: File containing a list of reference fasta paths
       pattern: "*.txt"
-
 output:
   ani:
     - - meta:
@@ -79,7 +76,6 @@ output:
         pattern: "versions.yml"
         ontologies:
           - edam: http://edamontology.org/format_3750
-
 authors:
   - "@Ethan-Hetrick"
   - "@abhi18av"

From b454c82b09738bfea953bd4d2d62712e93fac07e Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 15:00:42 -0500
Subject: [PATCH 06/41] fix: added newline

---
 modules/nf-core/fastani/main.nf | 1 +
 1 file changed, 1 insertion(+)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index f33cbbc1d5bb..93291f8466dd 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -57,3 +57,4 @@ process FASTANI {
     END_VERSIONS
     """
 }
+

From c0979e174a827544919cdce040e1dc3a5d743297 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 15:13:41 -0500
Subject: [PATCH 07/41] fix: attempt 2 at fixing whitespaces

---
 modules/nf-core/fastani/main.nf | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 93291f8466dd..fbc8142bea3b 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -28,14 +28,13 @@ process FASTANI {
     def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all')
     def input_query     = query ? "-q ${query}": "--ql ${ql}"
     def input_reference = reference ? "-r ${reference}": "--rl ${rl}"
-    
     """
     fastANI \\
         $input_query \\
         $input_reference \\
         --threads $task.cpus \\
         -o ${prefix}_v_${prefix2}.txt
-    
+        
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
@@ -45,7 +44,6 @@ process FASTANI {
     stub:
     def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
     def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all')
-
     """
     touch ${prefix}_v_${prefix2}.visual
     touch ${prefix}_v_${prefix2}.txt

From 49bbc990e8a61566f2c7e1c13576aece8efab1fc Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 15:20:55 -0500
Subject: [PATCH 08/41] fix: attempt 3 at fixing whitespaces

---
 modules/nf-core/fastani/main.nf | 3 +--
 1 file changed, 1 insertion(+), 2 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index fbc8142bea3b..eba7fa7575c7 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -34,7 +34,7 @@ process FASTANI {
         $input_reference \\
         --threads $task.cpus \\
         -o ${prefix}_v_${prefix2}.txt
-        
+
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":
         fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
@@ -55,4 +55,3 @@ process FASTANI {
     END_VERSIONS
     """
 }
-

From 41624465e47afd2a08880f42d0e0745cb1f965fe Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 17 Dec 2025 15:57:44 -0500
Subject: [PATCH 09/41] fix: formatting

---
 modules/nf-core/fastani/meta.yml           | 10 +++++-----
 modules/nf-core/fastani/tests/main.nf.test |  2 +-
 2 files changed, 6 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index b706814f994f..1dcb2ee823a4 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -15,10 +15,10 @@ tools:
       identifier: biotools:fastani
 input:
   - - meta:
-          type: map
-          description: |
-            Groovy Map containing sample information
-            e.g. [ id:'test' ]
+        type: map
+        description: |
+          Groovy Map containing sample information
+          e.g. [ id:'test' ]
     - query:
         type: file
         description: Fasta file to be used as the query
@@ -81,4 +81,4 @@ authors:
   - "@abhi18av"
 maintainers:
   - "@Ethan-Hetrick"
-  - "@abhi18av"
\ No newline at end of file
+  - "@abhi18av"
diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index b2f67e55513a..252283540d5e 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -64,4 +64,4 @@ nextflow_process {
 
     }
 
-}
\ No newline at end of file
+}

From 03ceb91366a0d0b2796f3aca8d408035fcaff85a Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Thu, 18 Dec 2025 13:23:55 -0500
Subject: [PATCH 10/41] Update modules/nf-core/fastani/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/meta.yml | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index 1dcb2ee823a4..53ba5b495bce 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -77,8 +77,8 @@ output:
         ontologies:
           - edam: http://edamontology.org/format_3750
 authors:
-  - "@Ethan-Hetrick"
   - "@abhi18av"
-maintainers:
   - "@Ethan-Hetrick"
+maintainers:
   - "@abhi18av"
+  - "@Ethan-Hetrick"

From 1b184c3815e23c5dee57810496b7b441d30818f2 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Thu, 18 Dec 2025 13:24:34 -0500
Subject: [PATCH 11/41] Update modules/nf-core/fastani/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/tests/main.nf.test | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index 252283540d5e..7d9415f4366e 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -6,7 +6,10 @@ nextflow_process {
     tag "fastani"
     script "../main.nf"
     process "FASTANI"
-
+    config "./nextflow.config"
+    tag "modules"
+    tag "modules_nfcore"
+    tag "fastani"
     test("fastani - 1v1") {
 
         when {

From b2f8b6658c01b8e02144c101628e9f20958f1bee Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Thu, 18 Dec 2025 13:24:46 -0500
Subject: [PATCH 12/41] Update modules/nf-core/fastani/main.nf

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index eba7fa7575c7..4323eb176f2b 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -33,7 +33,7 @@ process FASTANI {
         $input_query \\
         $input_reference \\
         --threads $task.cpus \\
-        -o ${prefix}_v_${prefix2}.txt
+        -o ${prefix}.txt
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From cd935a6347954e9f4c904ea74c37ed64d379b43a Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Thu, 18 Dec 2025 13:25:44 -0500
Subject: [PATCH 13/41] Update modules/nf-core/fastani/main.nf

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 4323eb176f2b..b9f168f456ee 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -24,7 +24,7 @@ process FASTANI {
 
     script:
     def args            = task.ext.args ?: ''
-    def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
+    def prefix = task.ext.prefix ?: "${meta.id}"
     def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all')
     def input_query     = query ? "-q ${query}": "--ql ${ql}"
     def input_reference = reference ? "-r ${reference}": "--rl ${rl}"

From bd45cca163ce94fab176a8b2d7ba11607b9177de Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Tue, 23 Dec 2025 13:42:58 -0500
Subject: [PATCH 14/41] reverted changes to prefixes to properly accommodate a
 multi-way comparison

---
 modules/nf-core/fastani/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index b9f168f456ee..a2e7f4ea72e1 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -24,8 +24,8 @@ process FASTANI {
 
     script:
     def args            = task.ext.args ?: ''
-    def prefix = task.ext.prefix ?: "${meta.id}"
-    def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all')
+    def prefix          = task.ext.prefix ?: ( meta.id ?: 'all' )
+    def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all' )
     def input_query     = query ? "-q ${query}": "--ql ${ql}"
     def input_reference = reference ? "-r ${reference}": "--rl ${rl}"
     """

From b60c343c8b46c1aaf8bbaea48efd135f723be7c6 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Tue, 23 Dec 2025 13:49:48 -0500
Subject: [PATCH 15/41] Renamed test to be more descriptive

---
 modules/nf-core/fastani/tests/main.nf.test | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index 7d9415f4366e..41cb6dbe60bd 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -10,7 +10,7 @@ nextflow_process {
     tag "modules"
     tag "modules_nfcore"
     tag "fastani"
-    test("fastani - 1v1") {
+    test("sarscov2 - referece vs contigs - fastANI") {
 
         when {
             process {

From fe4727687e3fed73429608a3b2612ed98a338114 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Tue, 23 Dec 2025 14:02:37 -0500
Subject: [PATCH 16/41] Fixed whitespaces

---
 modules/nf-core/fastani/meta.yml | 22 +++++++++++++++++++---
 1 file changed, 19 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index 53ba5b495bce..a0f73d9f2b0a 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -22,22 +22,30 @@ input:
     - query:
         type: file
         description: Fasta file to be used as the query
-        pattern: "*.fasta"
+        pattern: "*.{fasta,fna,fa}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
   - - meta2:
         type: map
         description: Groovy Map containing sample information for the reference
     - reference:
         type: file
         description: Fasta file to be used as the reference
-        pattern: "*.fasta"
+        pattern: "*.{fasta,fna,fa}"
+        ontologies:
+          - edam: http://edamontology.org/format_1929 # FASTA
   - ql:
       type: file
       description: File containing a list of query fasta paths
       pattern: "*.txt"
+      ontologies:
+        - edam: "http://edamontology.org/format_2330" # TXT
   - rl:
       type: file
       description: File containing a list of reference fasta paths
       pattern: "*.txt"
+      ontologies:
+        - edam: "http://edamontology.org/format_2330" # TXT
 output:
   ani:
     - - meta:
@@ -49,6 +57,8 @@ output:
           type: file
           description: ANI results file
           pattern: "*.txt"
+          ontologies:
+            - edam: "http://edamontology.org/format_2330" # TXT
   visual:
     - - meta:
           type: map
@@ -59,6 +69,9 @@ output:
           type: file
           optional: true
           description: FastANI visualization output
+          pattern: "*.visual"
+          ontologies:
+            - edam: "http://edamontology.org/format_3475" # TSV
   matrix:
     - - meta:
           type: map
@@ -69,13 +82,16 @@ output:
           type: file
           optional: true
           description: ANI matrix output
+          ontologies:
+            - edam: "http://edamontology.org/format_3033" # MATRIX
+
   versions:
     - versions.yml:
         type: file
         description: File containing software version information
         pattern: "versions.yml"
         ontologies:
-          - edam: http://edamontology.org/format_3750
+          - edam: http://edamontology.org/format_3750 # YAML
 authors:
   - "@abhi18av"
   - "@Ethan-Hetrick"

From b064fed343f5036577bd667825d1ac57b780107d Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Tue, 23 Dec 2025 14:17:48 -0500
Subject: [PATCH 17/41] ran nf-test

---
 .../nf-core/fastani/tests/main.nf.test.snap   | 45 +++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/modules/nf-core/fastani/tests/main.nf.test.snap b/modules/nf-core/fastani/tests/main.nf.test.snap
index 62ebcf259dd8..ed2dcb6b2968 100644
--- a/modules/nf-core/fastani/tests/main.nf.test.snap
+++ b/modules/nf-core/fastani/tests/main.nf.test.snap
@@ -176,5 +176,50 @@
             "nextflow": "25.10.1"
         },
         "timestamp": "2025-12-17T13:46:15.662109587"
+    },
+    "sarscov2 - referece vs contigs - fastANI": {
+        "content": [
+            {
+                "0": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
+                    ]
+                ],
+                "1": [
+                    
+                ],
+                "2": [
+                    
+                ],
+                "3": [
+                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                ],
+                "ani": [
+                    [
+                        {
+                            "id": "test"
+                        },
+                        "test.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
+                    ]
+                ],
+                "matrix": [
+                    
+                ],
+                "versions": [
+                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                ],
+                "visual": [
+                    
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.1"
+        },
+        "timestamp": "2025-12-23T14:17:10.557521793"
     }
 }
\ No newline at end of file

From 979d31f2d36ac0d6f971df35a01a85f6f8361dbb Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 15:20:01 -0500
Subject: [PATCH 18/41] refactor: updated how tool version was output

---
 modules/nf-core/fastani/main.nf | 7 +------
 1 file changed, 1 insertion(+), 6 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index a2e7f4ea72e1..e1cdf3347b63 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -17,7 +17,7 @@ process FASTANI {
     tuple val(meta), path("*.txt")      , emit: ani
     tuple val(meta), path("*.visual")   , optional:true , emit: visual
     tuple val(meta), path("*.matrix")   , optional:true , emit: matrix
-    path "versions.yml"                 , emit: versions
+    tuple val("${task.process}"), val("fastani"), eval('fastANI --version'), topic: versions, emit: versions_fastani
 
     when:
     task.ext.when == null || task.ext.when
@@ -34,11 +34,6 @@ process FASTANI {
         $input_reference \\
         --threads $task.cpus \\
         -o ${prefix}.txt
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
-    END_VERSIONS
     """
 
     stub:

From 2c8c45119722a3b5215a994cb2bd9c62c811fb48 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Wed, 14 Jan 2026 15:23:57 -0500
Subject: [PATCH 19/41] Update modules/nf-core/fastani/main.nf

Modified outputs to be named based on first prefix

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/main.nf | 7 +++----
 1 file changed, 3 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index e1cdf3347b63..ffcb92610961 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -38,11 +38,10 @@ process FASTANI {
 
     stub:
     def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
-    def prefix2         = task.ext.prefix2 ?: ( meta2.id ?: 'all')
     """
-    touch ${prefix}_v_${prefix2}.visual
-    touch ${prefix}_v_${prefix2}.txt
-    touch ${prefix}_v_${prefix2}.matrix
+    touch ${prefix}.visual
+    touch ${prefix}.txt
+    touch ${prefix}.matrix
 
     cat <<-END_VERSIONS > versions.yml
     "${task.process}":

From d9f49226a8476b24aab967b17f625f457e7d6251 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 15:25:38 -0500
Subject: [PATCH 20/41] fix: removed redundant tags in nf test script

---
 modules/nf-core/fastani/tests/main.nf.test | 3 ---
 1 file changed, 3 deletions(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index 41cb6dbe60bd..da7dddf1f210 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -7,9 +7,6 @@ nextflow_process {
     script "../main.nf"
     process "FASTANI"
     config "./nextflow.config"
-    tag "modules"
-    tag "modules_nfcore"
-    tag "fastani"
     test("sarscov2 - referece vs contigs - fastANI") {
 
         when {

From c1fb69aa0fd296dfb1aa79d661003b66fa111436 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 15:35:13 -0500
Subject: [PATCH 21/41] refactor: added new version syntax to stub as well

---
 modules/nf-core/fastani/main.nf | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index ffcb92610961..56d43e0089c7 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -38,14 +38,10 @@ process FASTANI {
 
     stub:
     def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
+    tuple val("${task.process}"), val("fastani"), eval('fastANI --version'), topic: versions, emit: versions_fastani
     """
     touch ${prefix}.visual
     touch ${prefix}.txt
     touch ${prefix}.matrix
-
-    cat <<-END_VERSIONS > versions.yml
-    "${task.process}":
-        fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
-    END_VERSIONS
     """
 }

From 7df07cd3b57ed9f1f71cf79325d6589b474d36e3 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 15:37:34 -0500
Subject: [PATCH 22/41] fix: fixed snapshot to capture new version syntax

---
 modules/nf-core/fastani/tests/main.nf.test | 18 ++++++++++++------
 1 file changed, 12 insertions(+), 6 deletions(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index da7dddf1f210..7bbbc584819b 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -27,9 +27,11 @@ nextflow_process {
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+            assertAll (
+                { assert snapshot(
+                    process.out.ani,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
             )
         }
     }
@@ -56,9 +58,13 @@ nextflow_process {
         }
 
         then {
-            assertAll(
-                { assert process.success },
-                { assert snapshot(process.out).match() }
+            assertAll (
+                { assert snapshot(
+                    process.out.ani,
+                    process.out.visual,
+                    process.out.matrix,
+                    process.out.findAll { key, val -> key.startsWith("versions")}
+                ).match() }
             )
         }
 

From 75801b99341a2d68bfebadbf410840ea2fa1b5ae Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 16:42:05 -0500
Subject: [PATCH 23/41] feature: added all v all mode test

---
 modules/nf-core/fastani/main.nf               |   1 -
 modules/nf-core/fastani/tests/main.nf.test    |  50 +++++-
 .../nf-core/fastani/tests/main.nf.test.snap   | 155 +++++++++++++-----
 3 files changed, 154 insertions(+), 52 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 56d43e0089c7..94b69c43cbfd 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -38,7 +38,6 @@ process FASTANI {
 
     stub:
     def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
-    tuple val("${task.process}"), val("fastani"), eval('fastANI --version'), topic: versions, emit: versions_fastani
     """
     touch ${prefix}.visual
     touch ${prefix}.txt
diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index 7bbbc584819b..afc266dcc42c 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -7,7 +7,7 @@ nextflow_process {
     script "../main.nf"
     process "FASTANI"
     config "./nextflow.config"
-    test("sarscov2 - referece vs contigs - fastANI") {
+    test("sarscov2 - referece vs contigs - fastANI - 1 v 1 mode") {
 
         when {
             process {
@@ -36,6 +36,47 @@ nextflow_process {
         }
     }
 
+    test("sarscov2 - referece vs contigs - fastANI - all vs all mode") {
+
+        when {
+            process {
+                """
+                def q_src = file(params.modules_testdata_base_path + 'genomics/sarscov2/genome/genome.fasta', checkIfExists: true)
+                def r_src = file(params.modules_testdata_base_path + 'genomics/sarscov2/illumina/fasta/contigs.fasta', checkIfExists: true)
+
+                // stage into the nf-test execution directory
+                def q_stage = new File(workDir.toString(), 'query.fasta')
+                def r_stage = new File(workDir.toString(), 'ref.fasta')
+
+                // Ensures files are staged locally
+                q_stage.bytes = q_src.bytes
+                r_stage.bytes = r_src.bytes
+
+                // create ql/rl list files
+                def ql_file = new File(workDir.toString(), 'query.list')
+                def rl_file = new File(workDir.toString(), 'reference.list')
+
+                ql_file.text = q_stage.getAbsolutePath() + System.lineSeparator()
+                rl_file.text = r_stage.getAbsolutePath() + System.lineSeparator()
+
+                input[0] = [ [], [] ]
+                input[1] = [ [], [] ]
+                input[2] = file( ql_file.getAbsolutePath(), checkIfExists: true )
+                input[3] = file( rl_file.getAbsolutePath(), checkIfExists: true )
+                """
+            }
+        }
+
+        then {
+            assertAll(
+                { assert snapshot(
+                    process.out.ani,
+                    process.out.findAll { key, val -> key.startsWith("versions") }
+                ).match() }
+            )
+        }
+    }
+
     test("stub") {
 
         options '-stub'
@@ -59,12 +100,7 @@ nextflow_process {
 
         then {
             assertAll (
-                { assert snapshot(
-                    process.out.ani,
-                    process.out.visual,
-                    process.out.matrix,
-                    process.out.findAll { key, val -> key.startsWith("versions")}
-                ).match() }
+                { assert snapshot(process.out).match() }
             )
         }
 
diff --git a/modules/nf-core/fastani/tests/main.nf.test.snap b/modules/nf-core/fastani/tests/main.nf.test.snap
index ed2dcb6b2968..a8afde4ef90f 100644
--- a/modules/nf-core/fastani/tests/main.nf.test.snap
+++ b/modules/nf-core/fastani/tests/main.nf.test.snap
@@ -77,6 +77,58 @@
         },
         "timestamp": "2023-10-18T12:02:08.983912093"
     },
+    "all vs all": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "all.txt:md5,c61ee10de3f2392ca02974c1b6536e77"
+                ]
+            ],
+            {
+                "versions_fastani": [
+                    [
+                        "FASTANI",
+                        "fastani",
+                        ""
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-14T16:28:57.910154362"
+    },
+    "sarscov2 - referece vs contigs - fastANI - 1 v 1 mode": {
+        "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
+                ]
+            ],
+            {
+                "versions_fastani": [
+                    [
+                        "FASTANI",
+                        "fastani",
+                        ""
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-14T16:41:18.165298623"
+    },
     "fastani - updates - fasta - fasta": {
         "content": [
             {
@@ -112,6 +164,32 @@
         },
         "timestamp": "2025-12-17T13:04:20.452047779"
     },
+    "sarscov2 - referece vs contigs - fastANI - all vs all mode": {
+        "content": [
+            [
+                [
+                    [
+                        
+                    ],
+                    "all.txt:md5,579bc0b0bb446422bf32b70ace54406e"
+                ]
+            ],
+            {
+                "versions_fastani": [
+                    [
+                        "FASTANI",
+                        "fastani",
+                        ""
+                    ]
+                ]
+            }
+        ],
+        "meta": {
+            "nf-test": "0.9.3",
+            "nextflow": "25.10.2"
+        },
+        "timestamp": "2026-01-14T16:41:28.292554801"
+    },
     "stub": {
         "content": [
             {
@@ -120,7 +198,7 @@
                         {
                             "id": "test"
                         },
-                        "test_v_test2.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "1": [
@@ -128,7 +206,7 @@
                         {
                             "id": "test"
                         },
-                        "test_v_test2.visual:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.visual:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "2": [
@@ -136,18 +214,22 @@
                         {
                             "id": "test"
                         },
-                        "test_v_test2.matrix:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.matrix:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "3": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                    [
+                        "FASTANI",
+                        "fastani",
+                        ""
+                    ]
                 ],
                 "ani": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_v_test2.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.txt:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
                 "matrix": [
@@ -155,71 +237,56 @@
                         {
                             "id": "test"
                         },
-                        "test_v_test2.matrix:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.matrix:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ],
-                "versions": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
+                "versions_fastani": [
+                    [
+                        "FASTANI",
+                        "fastani",
+                        ""
+                    ]
                 ],
                 "visual": [
                     [
                         {
                             "id": "test"
                         },
-                        "test_v_test2.visual:md5,d41d8cd98f00b204e9800998ecf8427e"
+                        "test.visual:md5,d41d8cd98f00b204e9800998ecf8427e"
                     ]
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.1"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-17T13:46:15.662109587"
+        "timestamp": "2026-01-14T16:39:38.8147991"
     },
     "sarscov2 - referece vs contigs - fastANI": {
         "content": [
+            [
+                [
+                    {
+                        "id": "test"
+                    },
+                    "test.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
+                ]
+            ],
             {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
-                ],
-                "ani": [
+                "versions_fastani": [
                     [
-                        {
-                            "id": "test"
-                        },
-                        "test.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
+                        "FASTANI",
+                        "fastani",
+                        ""
                     ]
-                ],
-                "matrix": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
-                ],
-                "visual": [
-                    
                 ]
             }
         ],
         "meta": {
             "nf-test": "0.9.3",
-            "nextflow": "25.10.1"
+            "nextflow": "25.10.2"
         },
-        "timestamp": "2025-12-23T14:17:10.557521793"
+        "timestamp": "2026-01-14T15:39:54.132926413"
     }
 }
\ No newline at end of file

From 8c8f5fa62a5ee2773159cb48bca0f8d37331e3bf Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 16:47:52 -0500
Subject: [PATCH 24/41] chore: updated meta.yml to clarify input priority

---
 modules/nf-core/fastani/meta.yml | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index a0f73d9f2b0a..7b69c1b02ab2 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -21,7 +21,7 @@ input:
           e.g. [ id:'test' ]
     - query:
         type: file
-        description: Fasta file to be used as the query
+        description: Fasta file to be used as the query. If provided, ql will be ignored.
         pattern: "*.{fasta,fna,fa}"
         ontologies:
           - edam: http://edamontology.org/format_1929 # FASTA
@@ -30,19 +30,19 @@ input:
         description: Groovy Map containing sample information for the reference
     - reference:
         type: file
-        description: Fasta file to be used as the reference
+        description: Fasta file to be used as the reference. If provided, rl will be ignored.
         pattern: "*.{fasta,fna,fa}"
         ontologies:
           - edam: http://edamontology.org/format_1929 # FASTA
   - ql:
       type: file
-      description: File containing a list of query fasta paths
+      description: File containing a list of query fasta paths. query input takes precedence over this list if both are provided.
       pattern: "*.txt"
       ontologies:
         - edam: "http://edamontology.org/format_2330" # TXT
   - rl:
       type: file
-      description: File containing a list of reference fasta paths
+      description: File containing a list of reference fasta paths. reference input takes precedence over this list if both are provided.
       pattern: "*.txt"
       ontologies:
         - edam: "http://edamontology.org/format_2330" # TXT

From 523e1dd3158248dc59ff24193dd7eb6bc7905cf4 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 16:50:04 -0500
Subject: [PATCH 25/41] chore: fixed whitespaces

---
 modules/nf-core/fastani/main.nf | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 94b69c43cbfd..195ad496470b 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -14,9 +14,9 @@ process FASTANI {
     path(rl)
 
     output:
-    tuple val(meta), path("*.txt")      , emit: ani
-    tuple val(meta), path("*.visual")   , optional:true , emit: visual
-    tuple val(meta), path("*.matrix")   , optional:true , emit: matrix
+    tuple val(meta), path("*.txt")   , emit: ani
+    tuple val(meta), path("*.visual"), optional:true , emit: visual
+    tuple val(meta), path("*.matrix"), optional:true , emit: matrix
     tuple val("${task.process}"), val("fastani"), eval('fastANI --version'), topic: versions, emit: versions_fastani
 
     when:

From 9d1c320be74a1f8d652359444c0db1d2d10a8775 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 16:50:36 -0500
Subject: [PATCH 26/41] chore: fixed whitespaces

---
 modules/nf-core/fastani/main.nf | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 195ad496470b..5bc5066400d1 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -15,8 +15,8 @@ process FASTANI {
 
     output:
     tuple val(meta), path("*.txt")   , emit: ani
-    tuple val(meta), path("*.visual"), optional:true , emit: visual
-    tuple val(meta), path("*.matrix"), optional:true , emit: matrix
+    tuple val(meta), path("*.visual"), optional:true, emit: visual
+    tuple val(meta), path("*.matrix"), optional:true, emit: matrix
     tuple val("${task.process}"), val("fastani"), eval('fastANI --version'), topic: versions, emit: versions_fastani
 
     when:

From 1c042d6be6adda32c33b3386d757b104288e584f Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Wed, 14 Jan 2026 17:14:23 -0500
Subject: [PATCH 27/41] fix: addressed nf-core lint errors and updated fastani
 version

---
 modules/nf-core/fastani/environment.yml |  2 +-
 modules/nf-core/fastani/main.nf         |  4 ++--
 modules/nf-core/fastani/meta.yml        | 18 ++++++++++--------
 3 files changed, 13 insertions(+), 11 deletions(-)

diff --git a/modules/nf-core/fastani/environment.yml b/modules/nf-core/fastani/environment.yml
index 25c0180f0496..5fd0c120c257 100644
--- a/modules/nf-core/fastani/environment.yml
+++ b/modules/nf-core/fastani/environment.yml
@@ -4,4 +4,4 @@ channels:
   - conda-forge
   - bioconda
 dependencies:
-  - bioconda::fastani=1.32
+  - bioconda::fastani=1.34
diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 5bc5066400d1..e56ddc5053b9 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -4,8 +4,8 @@ process FASTANI {
 
     conda "${moduleDir}/environment.yml"
     container "${ workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ?
-        'https://depot.galaxyproject.org/singularity/fastani:1.32--he1c1bb9_0' :
-        'biocontainers/fastani:1.32--he1c1bb9_0' }"
+        'https://depot.galaxyproject.org/singularity/fastani:1.34--hb66fcc3_7' :
+        'biocontainers/fastani:1.34--hb66fcc3_7' }"
 
     input:
     tuple val(meta),  path(query)
diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index 7b69c1b02ab2..feb0e7657662 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -84,14 +84,16 @@ output:
           description: ANI matrix output
           ontologies:
             - edam: "http://edamontology.org/format_3033" # MATRIX
-
-  versions:
-    - versions.yml:
-        type: file
-        description: File containing software version information
-        pattern: "versions.yml"
-        ontologies:
-          - edam: http://edamontology.org/format_3750 # YAML
+  versions_fastani:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fastani:
+          type: string
+          description: The name of the tool
+      - fastANI --version:
+          type: eval
+          description: The expression to obtain the version of the tool
 authors:
   - "@abhi18av"
   - "@Ethan-Hetrick"

From e28e09ab82e93dbe8b65580a5bf0d595110283db Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Thu, 12 Feb 2026 17:20:02 -0500
Subject: [PATCH 28/41] Update modules/nf-core/fastani/tests/main.nf.test

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/tests/main.nf.test | 7 ++++++-
 1 file changed, 6 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index afc266dcc42c..ced2ad40b778 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -5,7 +5,12 @@ nextflow_process {
     tag "modules"
     tag "fastani"
     script "../main.nf"
-    process "FASTANI"
+name "Test Process FASTANI"
+tag "modules_nfcore"
+tag "modules"
+tag "fastani"
+script "../main.nf"
+process "FASTANI"
     config "./nextflow.config"
     test("sarscov2 - referece vs contigs - fastANI - 1 v 1 mode") {
 

From 349844ef879e80b9226782e3fa8f5344b36a4a83 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Thu, 12 Feb 2026 17:55:46 -0500
Subject: [PATCH 29/41] fix: removed accidental commit

---
 modules/nf-core/fastani/main.nf | 27 ---------------------------
 1 file changed, 27 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 8353dc143090..e56ddc5053b9 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -43,31 +43,4 @@ process FASTANI {
     touch ${prefix}.txt
     touch ${prefix}.matrix
     """
-    def prefix = task.ext.prefix ?: "${meta.id}"
-
-    if (meta.batch_input) {
-        """
-        fastANI \\
-            -ql $query \\
-            -rl $reference \\
-            -o ${prefix}.ani.txt
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
-        END_VERSIONS
-        """
-    } else {
-        """
-        fastANI \\
-            -q $query \\
-            -r $reference \\
-            -o ${prefix}.ani.txt
-
-        cat <<-END_VERSIONS > versions.yml
-        "${task.process}":
-            fastani: \$(fastANI --version 2>&1 | sed 's/version//;')
-        END_VERSIONS
-        """
-    }
 }

From d9023c5f5972c33f437aebb6b238b24c1f776c24 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Thu, 12 Feb 2026 18:09:07 -0500
Subject: [PATCH 30/41] fix: corrected improper version capture

---
 modules/nf-core/fastani/main.nf | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index e56ddc5053b9..a689c31c8d19 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -17,7 +17,7 @@ process FASTANI {
     tuple val(meta), path("*.txt")   , emit: ani
     tuple val(meta), path("*.visual"), optional:true, emit: visual
     tuple val(meta), path("*.matrix"), optional:true, emit: matrix
-    tuple val("${task.process}"), val("fastani"), eval('fastANI --version'), topic: versions, emit: versions_fastani
+    tuple val("${task.process}"), val("fastani"), eval('fastANI --version 2>&1 | head -1 | sed "s/version\ //"'), topic: versions, emit: versions_fastani
 
     when:
     task.ext.when == null || task.ext.when

From 43d6ed31a154e1aeb6587a6011c97aa046935361 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Thu, 12 Feb 2026 18:22:48 -0500
Subject: [PATCH 31/41] chore: update snapshot

---
 modules/nf-core/fastani/main.nf               |  2 +-
 modules/nf-core/fastani/meta.yml              | 45 +++++++++++++------
 .../nf-core/fastani/tests/main.nf.test.snap   | 14 +++---
 3 files changed, 39 insertions(+), 22 deletions(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index a689c31c8d19..9f4ca7279e9a 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -17,7 +17,7 @@ process FASTANI {
     tuple val(meta), path("*.txt")   , emit: ani
     tuple val(meta), path("*.visual"), optional:true, emit: visual
     tuple val(meta), path("*.matrix"), optional:true, emit: matrix
-    tuple val("${task.process}"), val("fastani"), eval('fastANI --version 2>&1 | head -1 | sed "s/version\ //"'), topic: versions, emit: versions_fastani
+    tuple val("${task.process}"), val("fastani"), eval('fastANI --version 2>&1 | head -1 | sed "s/version\\ //"'), topic: versions, emit: versions_fastani
 
     when:
     task.ext.when == null || task.ext.when
diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index feb0e7657662..fe57b0588684 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -6,12 +6,14 @@ keywords:
   - ANI
 tools:
   - fastani:
-      description: FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI).
+      description: FastANI is developed for fast alignment-free computation of
+        whole-genome Average Nucleotide Identity (ANI).
       homepage: https://github.com/ParBLiSS/FastANI
       documentation: https://github.com/ParBLiSS/FastANI
       tool_dev_url: https://github.com/ParBLiSS/FastANI
       doi: 10.1038/s41467-018-07641-9
-      licence: ["Apache-2.0"]
+      licence:
+        - "Apache-2.0"
       identifier: biotools:fastani
 input:
   - - meta:
@@ -21,31 +23,35 @@ input:
           e.g. [ id:'test' ]
     - query:
         type: file
-        description: Fasta file to be used as the query. If provided, ql will be ignored.
+        description: Fasta file to be used as the query. If provided, ql will be
+          ignored.
         pattern: "*.{fasta,fna,fa}"
         ontologies:
-          - edam: http://edamontology.org/format_1929 # FASTA
+          - edam: http://edamontology.org/format_1929
   - - meta2:
         type: map
         description: Groovy Map containing sample information for the reference
     - reference:
         type: file
-        description: Fasta file to be used as the reference. If provided, rl will be ignored.
+        description: Fasta file to be used as the reference. If provided, rl will
+          be ignored.
         pattern: "*.{fasta,fna,fa}"
         ontologies:
-          - edam: http://edamontology.org/format_1929 # FASTA
+          - edam: http://edamontology.org/format_1929
   - ql:
       type: file
-      description: File containing a list of query fasta paths. query input takes precedence over this list if both are provided.
+      description: File containing a list of query fasta paths. query input takes
+        precedence over this list if both are provided.
       pattern: "*.txt"
       ontologies:
-        - edam: "http://edamontology.org/format_2330" # TXT
+        - edam: "http://edamontology.org/format_2330"
   - rl:
       type: file
-      description: File containing a list of reference fasta paths. reference input takes precedence over this list if both are provided.
+      description: File containing a list of reference fasta paths. reference
+        input takes precedence over this list if both are provided.
       pattern: "*.txt"
       ontologies:
-        - edam: "http://edamontology.org/format_2330" # TXT
+        - edam: "http://edamontology.org/format_2330"
 output:
   ani:
     - - meta:
@@ -58,7 +64,7 @@ output:
           description: ANI results file
           pattern: "*.txt"
           ontologies:
-            - edam: "http://edamontology.org/format_2330" # TXT
+            - edam: "http://edamontology.org/format_2330"
   visual:
     - - meta:
           type: map
@@ -71,7 +77,7 @@ output:
           description: FastANI visualization output
           pattern: "*.visual"
           ontologies:
-            - edam: "http://edamontology.org/format_3475" # TSV
+            - edam: "http://edamontology.org/format_3475"
   matrix:
     - - meta:
           type: map
@@ -83,7 +89,7 @@ output:
           optional: true
           description: ANI matrix output
           ontologies:
-            - edam: "http://edamontology.org/format_3033" # MATRIX
+            - edam: "http://edamontology.org/format_3033"
   versions_fastani:
     - - ${task.process}:
           type: string
@@ -91,7 +97,18 @@ output:
       - fastani:
           type: string
           description: The name of the tool
-      - fastANI --version:
+      - fastANI --version 2>&1 | head -1 | sed "s/version\ //":
+          type: eval
+          description: The expression to obtain the version of the tool
+topics:
+  versions:
+    - - ${task.process}:
+          type: string
+          description: The name of the process
+      - fastani:
+          type: string
+          description: The name of the tool
+      - fastANI --version 2>&1 | head -1 | sed "s/version\ //":
           type: eval
           description: The expression to obtain the version of the tool
 authors:
diff --git a/modules/nf-core/fastani/tests/main.nf.test.snap b/modules/nf-core/fastani/tests/main.nf.test.snap
index a8afde4ef90f..6beec3b7aa50 100644
--- a/modules/nf-core/fastani/tests/main.nf.test.snap
+++ b/modules/nf-core/fastani/tests/main.nf.test.snap
@@ -118,7 +118,7 @@
                     [
                         "FASTANI",
                         "fastani",
-                        ""
+                        "1.34"
                     ]
                 ]
             }
@@ -127,7 +127,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-14T16:41:18.165298623"
+        "timestamp": "2026-02-12T18:20:14.95813302"
     },
     "fastani - updates - fasta - fasta": {
         "content": [
@@ -179,7 +179,7 @@
                     [
                         "FASTANI",
                         "fastani",
-                        ""
+                        "1.34"
                     ]
                 ]
             }
@@ -188,7 +188,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-14T16:41:28.292554801"
+        "timestamp": "2026-02-12T18:20:23.079816301"
     },
     "stub": {
         "content": [
@@ -221,7 +221,7 @@
                     [
                         "FASTANI",
                         "fastani",
-                        ""
+                        "1.34"
                     ]
                 ],
                 "ani": [
@@ -244,7 +244,7 @@
                     [
                         "FASTANI",
                         "fastani",
-                        ""
+                        "1.34"
                     ]
                 ],
                 "visual": [
@@ -261,7 +261,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-01-14T16:39:38.8147991"
+        "timestamp": "2026-02-12T18:20:31.13425659"
     },
     "sarscov2 - referece vs contigs - fastANI": {
         "content": [

From fe9795cd2d14136490c532c5155213b372b7b5e3 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Thu, 12 Feb 2026 18:39:42 -0500
Subject: [PATCH 32/41] feature: made it to where query and reference lists
 contain both genomes

---
 modules/nf-core/fastani/tests/main.nf.test      | 9 +++++++--
 modules/nf-core/fastani/tests/main.nf.test.snap | 4 ++--
 2 files changed, 9 insertions(+), 4 deletions(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index ced2ad40b778..003f1c4bd134 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -61,8 +61,13 @@ process "FASTANI"
                 def ql_file = new File(workDir.toString(), 'query.list')
                 def rl_file = new File(workDir.toString(), 'reference.list')
 
-                ql_file.text = q_stage.getAbsolutePath() + System.lineSeparator()
-                rl_file.text = r_stage.getAbsolutePath() + System.lineSeparator()
+                ql_file.text =
+                    q_stage.getAbsolutePath() + System.lineSeparator() +
+                    r_stage.getAbsolutePath() + System.lineSeparator()
+
+                rl_file.text =
+                    q_stage.getAbsolutePath() + System.lineSeparator() +
+                    r_stage.getAbsolutePath() + System.lineSeparator()
 
                 input[0] = [ [], [] ]
                 input[1] = [ [], [] ]
diff --git a/modules/nf-core/fastani/tests/main.nf.test.snap b/modules/nf-core/fastani/tests/main.nf.test.snap
index 6beec3b7aa50..eb721bfeeee8 100644
--- a/modules/nf-core/fastani/tests/main.nf.test.snap
+++ b/modules/nf-core/fastani/tests/main.nf.test.snap
@@ -171,7 +171,7 @@
                     [
                         
                     ],
-                    "all.txt:md5,579bc0b0bb446422bf32b70ace54406e"
+                    "all.txt:md5,616c232d14c8f9ad3cda307154fa895e"
                 ]
             ],
             {
@@ -188,7 +188,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T18:20:23.079816301"
+        "timestamp": "2026-02-12T18:34:43.814618838"
     },
     "stub": {
         "content": [

From 2b4f0d03aec7f843221ae8044b1f138833d804d1 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Fri, 13 Feb 2026 12:13:58 -0500
Subject: [PATCH 33/41] Update modules/nf-core/fastani/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index fe57b0588684..bd05d51bf14d 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -77,7 +77,7 @@ output:
           description: FastANI visualization output
           pattern: "*.visual"
           ontologies:
-            - edam: "http://edamontology.org/format_3475"
+            - edam: "http://edamontology.org/format_3475" # TSV
   matrix:
     - - meta:
           type: map

From 8d4e36f1bc3decb2816370d4f4119bf742326e93 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Fri, 13 Feb 2026 12:14:52 -0500
Subject: [PATCH 34/41] Update modules/nf-core/fastani/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index bd05d51bf14d..ac1814e885a0 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -27,7 +27,7 @@ input:
           ignored.
         pattern: "*.{fasta,fna,fa}"
         ontologies:
-          - edam: http://edamontology.org/format_1929
+          - edam: http://edamontology.org/format_1929 # FASTA
   - - meta2:
         type: map
         description: Groovy Map containing sample information for the reference

From f37e8bbdad0fe9ff072d8df5b09e3286367fd0e8 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Fri, 13 Feb 2026 12:15:02 -0500
Subject: [PATCH 35/41] Update modules/nf-core/fastani/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index ac1814e885a0..304e141fd53b 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -51,7 +51,7 @@ input:
         input takes precedence over this list if both are provided.
       pattern: "*.txt"
       ontologies:
-        - edam: "http://edamontology.org/format_2330"
+        - edam: "http://edamontology.org/format_2330" # Textual format
 output:
   ani:
     - - meta:

From 08c9c2643e128fe2c620a1aae7d836f5826c5a41 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Fri, 13 Feb 2026 12:25:29 -0500
Subject: [PATCH 36/41] Update modules/nf-core/fastani/main.nf

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/main.nf | 5 ++++-
 1 file changed, 4 insertions(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/main.nf b/modules/nf-core/fastani/main.nf
index 9f4ca7279e9a..defe360892c2 100644
--- a/modules/nf-core/fastani/main.nf
+++ b/modules/nf-core/fastani/main.nf
@@ -37,8 +37,11 @@ process FASTANI {
     """
 
     stub:
-    def prefix          = task.ext.prefix  ?: ( meta.id  ?: 'all')
+    def args = task.ext.args ?: ''
+    def prefix = task.ext.prefix  ?: ( meta.id  ?: 'all')
     """
+    echo $args
+
     touch ${prefix}.visual
     touch ${prefix}.txt
     touch ${prefix}.matrix

From 3945985ffe315bdb77ab88b68b1a36d69be3c428 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Fri, 13 Feb 2026 12:25:38 -0500
Subject: [PATCH 37/41] Update modules/nf-core/fastani/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index 304e141fd53b..643b8aa60213 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -64,7 +64,7 @@ output:
           description: ANI results file
           pattern: "*.txt"
           ontologies:
-            - edam: "http://edamontology.org/format_2330"
+            - edam: "http://edamontology.org/format_2330" # Textual format
   visual:
     - - meta:
           type: map

From c762a360c560de7767cbc59699df98300af85de9 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <99049240+Ethan-Hetrick@users.noreply.github.com>
Date: Fri, 13 Feb 2026 12:25:54 -0500
Subject: [PATCH 38/41] Update modules/nf-core/fastani/meta.yml

Co-authored-by: Evangelos Karatzas <32259775+vagkaratzas@users.noreply.github.com>
---
 modules/nf-core/fastani/meta.yml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nf-core/fastani/meta.yml b/modules/nf-core/fastani/meta.yml
index 643b8aa60213..f7a1bd5f2c43 100644
--- a/modules/nf-core/fastani/meta.yml
+++ b/modules/nf-core/fastani/meta.yml
@@ -37,7 +37,7 @@ input:
           be ignored.
         pattern: "*.{fasta,fna,fa}"
         ontologies:
-          - edam: http://edamontology.org/format_1929
+          - edam: http://edamontology.org/format_1929 # FASTA
   - ql:
       type: file
       description: File containing a list of query fasta paths. query input takes

From 09bf7adbbb54701683f087c3e42ac58ee19a4a38 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Fri, 13 Feb 2026 12:36:06 -0500
Subject: [PATCH 39/41] chore: cleanup directives at top of nf.test

---
 modules/nf-core/fastani/tests/main.nf.test | 12 ++++--------
 1 file changed, 4 insertions(+), 8 deletions(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index 003f1c4bd134..9c9971b1c78b 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -1,17 +1,13 @@
 nextflow_process {
 
     name "Test Process FASTANI"
+    script "../main.nf"
+    process "FASTANI"
+    config "./nextflow.config"
     tag "modules_nfcore"
     tag "modules"
     tag "fastani"
-    script "../main.nf"
-name "Test Process FASTANI"
-tag "modules_nfcore"
-tag "modules"
-tag "fastani"
-script "../main.nf"
-process "FASTANI"
-    config "./nextflow.config"
+
     test("sarscov2 - referece vs contigs - fastANI - 1 v 1 mode") {
 
         when {

From 00098ca17a747e63733c321cc409e79e5cad38c3 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Fri, 13 Feb 2026 13:11:59 -0500
Subject: [PATCH 40/41] feature: added line count check for all v all mode

---
 modules/nf-core/fastani/tests/main.nf.test      | 14 ++++++++++----
 modules/nf-core/fastani/tests/main.nf.test.snap | 10 +---------
 2 files changed, 11 insertions(+), 13 deletions(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test b/modules/nf-core/fastani/tests/main.nf.test
index 9c9971b1c78b..e0cc590d6c91 100644
--- a/modules/nf-core/fastani/tests/main.nf.test
+++ b/modules/nf-core/fastani/tests/main.nf.test
@@ -29,6 +29,7 @@ nextflow_process {
 
         then {
             assertAll (
+                { assert process.success },
                 { assert snapshot(
                     process.out.ani,
                     process.out.findAll { key, val -> key.startsWith("versions")}
@@ -75,10 +76,14 @@ nextflow_process {
 
         then {
             assertAll(
-                { assert snapshot(
-                    process.out.ani,
-                    process.out.findAll { key, val -> key.startsWith("versions") }
-                ).match() }
+                { assert process.success },
+                {
+                    def aniFile = path(process.out.ani[0][1])
+                    assert aniFile.exists()
+                    def lines = aniFile.readLines()
+                    assert lines.size() == 4 : "Expected 4 ANI comparisons but found ${lines.size()}"
+                },
+                { assert snapshot(process.out.findAll { key, val -> key.startsWith("versions") }).match() }
             )
         }
     }
@@ -106,6 +111,7 @@ nextflow_process {
 
         then {
             assertAll (
+                { assert process.success },
                 { assert snapshot(process.out).match() }
             )
         }
diff --git a/modules/nf-core/fastani/tests/main.nf.test.snap b/modules/nf-core/fastani/tests/main.nf.test.snap
index eb721bfeeee8..7bbd7329a92b 100644
--- a/modules/nf-core/fastani/tests/main.nf.test.snap
+++ b/modules/nf-core/fastani/tests/main.nf.test.snap
@@ -166,14 +166,6 @@
     },
     "sarscov2 - referece vs contigs - fastANI - all vs all mode": {
         "content": [
-            [
-                [
-                    [
-                        
-                    ],
-                    "all.txt:md5,616c232d14c8f9ad3cda307154fa895e"
-                ]
-            ],
             {
                 "versions_fastani": [
                     [
@@ -188,7 +180,7 @@
             "nf-test": "0.9.3",
             "nextflow": "25.10.2"
         },
-        "timestamp": "2026-02-12T18:34:43.814618838"
+        "timestamp": "2026-02-13T12:46:56.303203093"
     },
     "stub": {
         "content": [

From 3f5a987a9d33284f192107fa732c8a00dec173a0 Mon Sep 17 00:00:00 2001
From: Ethan Hetrick <rqu4@cdc.gov>
Date: Fri, 13 Feb 2026 14:28:34 -0500
Subject: [PATCH 41/41] chore: removed obsolete nf-tests

---
 .../nf-core/fastani/tests/main.nf.test.snap   | 165 ------------------
 1 file changed, 165 deletions(-)

diff --git a/modules/nf-core/fastani/tests/main.nf.test.snap b/modules/nf-core/fastani/tests/main.nf.test.snap
index 7bbd7329a92b..cd94a57b9842 100644
--- a/modules/nf-core/fastani/tests/main.nf.test.snap
+++ b/modules/nf-core/fastani/tests/main.nf.test.snap
@@ -1,108 +1,4 @@
 {
-    "fastani - 1v1": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_v_test2.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
-                    ]
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
-                ],
-                "ani": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test_v_test2.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
-                    ]
-                ],
-                "matrix": [
-                    
-                ],
-                "versions": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
-                ],
-                "visual": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.1"
-        },
-        "timestamp": "2025-12-17T13:46:06.970355559"
-    },
-    "FastANI": {
-        "content": [
-            {
-                "0": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.ani.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
-                    ]
-                ],
-                "1": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
-                ],
-                "ani": [
-                    [
-                        {
-                            "id": "test"
-                        },
-                        "test.ani.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
-                    ]
-                ],
-                "versions": [
-                    "versions.yml:md5,6d40b0941a0753738f6c844eb8fc7c73"
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.1"
-        },
-        "timestamp": "2023-10-18T12:02:08.983912093"
-    },
-    "all vs all": {
-        "content": [
-            [
-                [
-                    [
-                        
-                    ],
-                    "all.txt:md5,c61ee10de3f2392ca02974c1b6536e77"
-                ]
-            ],
-            {
-                "versions_fastani": [
-                    [
-                        "FASTANI",
-                        "fastani",
-                        ""
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-14T16:28:57.910154362"
-    },
     "sarscov2 - referece vs contigs - fastANI - 1 v 1 mode": {
         "content": [
             [
@@ -129,41 +25,6 @@
         },
         "timestamp": "2026-02-12T18:20:14.95813302"
     },
-    "fastani - updates - fasta - fasta": {
-        "content": [
-            {
-                "0": [
-                    
-                ],
-                "1": [
-                    
-                ],
-                "2": [
-                    
-                ],
-                "3": [
-                    
-                ],
-                "ani": [
-                    
-                ],
-                "matrix": [
-                    
-                ],
-                "versions": [
-                    
-                ],
-                "visual": [
-                    
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.1"
-        },
-        "timestamp": "2025-12-17T13:04:20.452047779"
-    },
     "sarscov2 - referece vs contigs - fastANI - all vs all mode": {
         "content": [
             {
@@ -254,31 +115,5 @@
             "nextflow": "25.10.2"
         },
         "timestamp": "2026-02-12T18:20:31.13425659"
-    },
-    "sarscov2 - referece vs contigs - fastANI": {
-        "content": [
-            [
-                [
-                    {
-                        "id": "test"
-                    },
-                    "test.txt:md5,31d4f04e8cffe13080c86db3f9f3a589"
-                ]
-            ],
-            {
-                "versions_fastani": [
-                    [
-                        "FASTANI",
-                        "fastani",
-                        ""
-                    ]
-                ]
-            }
-        ],
-        "meta": {
-            "nf-test": "0.9.3",
-            "nextflow": "25.10.2"
-        },
-        "timestamp": "2026-01-14T15:39:54.132926413"
     }
 }
\ No newline at end of file